yes, using mats will scratch up the surface of the irons to some extent. no doubt we like to keep our clubs shiny, new and scratch free but as long as they dont hurt the performance of our game it should be fine. hahaha i remember coming home and wiping my clubs religiously... and theni got lazy and accepted the fact that it is inevitable for your clubs to get scratches here and there.
Also.. new indoor mats come with special (shall i say softer/ more shock absorbent) pad where you place the tee to protect the clubs from getting damaged